How to apply transformations to empties?
I found a solution:

You have to modify the empty's location, scale and rotation properties with the information contained in the Transformation Matrix. If you used vectors to build the Transformation Matrix, just apply them:

# For location add the vectors
empty.location = empty.location + traslationVect

# For scale assign the vector
empty.scale = scaleVector


If you have the transformation matrix you'll have to build the vectors based on the matrix's elements

PS: I didn't dive into rotations.